GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Desulfovibrio vulgaris Hildenborough

Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate 209297 para-aminobenzoate synthase, component I

Query= curated2:Q9HS66
         (488 letters)



>MicrobesOnline__882:209297
          Length = 334

 Score =  169 bits (427), Expect = 2e-46
 Identities = 113/293 (38%), Positives = 150/293 (51%), Gaps = 7/293 (2%)

Query: 180 QSLAAAIRDGDPAVGPPPADSPAPFESVAGRAAFESRVRRIQDAIRDGDTFQANVSHRLD 239
           + L+AA RDG  A G   A +            +   VR++  AIR GDT+Q N++ R  
Sbjct: 37  RGLSAAPRDGT-APGDDLALALDELVPSLDATTYPDGVRQVLAAIRRGDTYQLNLTSRFT 95

Query: 240 APAAVHPVAVFEA-LRDTNPAPYSGIVEFPGVDLVSASPELLLARRGRELTTEPIAGTR- 297
           A       A F   L    P P++  +      ++S SPE  L   G E+  +PI GTR 
Sbjct: 96  ARRPGMDAAAFLLRLWQQRPTPFAAYLHAGRHRILSLSPERFLRVGGGEVLAQPIKGTRS 155

Query: 298 --PRGATPAEDDAARAALRADDKERAEHAMLVDLERNDLGKVSEYGSVAVPDYRRVDAYS 355
             P   +P E     AALRAD KE AE +M+VDL RND+     Y SV VP +    A  
Sbjct: 156 FDPATTSPGERARLEAALRADPKEHAELSMVVDLLRNDISATCAYDSVRVPRHCATFAVG 215

Query: 356 EVLHLVSEVTGRLRDSCSLRDAIAAVFPGGTITGAPKPRTMALIDTVEATRRGPYTGSLA 415
            ++ + S+VTG LRD  +  D +   FPGG++TG PKPRTM+LI+ +E   R  Y GSL 
Sbjct: 216 PLIQMCSDVTGTLRDGTTCLDLLRHAFPGGSVTGCPKPRTMSLIERIEPHPRDVYCGSLV 275

Query: 416 AIGFDGDATLSITIRTLVRRAAT--YHLRVGAGIVHDSTPAAEYDETLAKARA 466
           A+    D   SI IRT +    T   HL  G+G+  DS P  EY ET+ K  A
Sbjct: 276 AVAGPRDMDSSIAIRTAMYDTTTGLLHLYAGSGLTVDSDPEGEYRETVDKTSA 328


Lambda     K      H
   0.317    0.135    0.397 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 530
Number of extensions: 36
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 488
Length of database: 334
Length adjustment: 31
Effective length of query: 457
Effective length of database: 303
Effective search space:   138471
Effective search space used:   138471
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory